PDB
9ME1
Resolution
3.4 Å
Released
Sept. 10, 2025
Receptor
CXCR4
Class
A
Species
Homo sapiens
Ligand
Stromal cell-derived factor 1
Function
Agonist
Reference
10.1038/S41467-025-63815-2

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Ligand Amino Acid Generic Number Segment Interaction Type
Stromal cell-derived factor 1 E26 N-term polar (charge-assisted hydrogen bond)
Stromal cell-derived factor 1 E26 N-term polar (hydrogen bond with backbone)
Stromal cell-derived factor 1 P27 N-term Van der Waals
Stromal cell-derived factor 1 C28 N-term Van der Waals
Stromal cell-derived factor 1 C28 N-term hydrophobic
Stromal cell-derived factor 1 F29 N-term hydrophobic
Stromal cell-derived factor 1 F29 N-term Van der Waals
Stromal cell-derived factor 1 R30 N-term polar (charge-assisted hydrogen bond)
Stromal cell-derived factor 1 W94 2.60x60 TM2 hydrophobic
Stromal cell-derived factor 1 W94 2.60x60 TM2 Van der Waals
Stromal cell-derived factor 1 H113 3.29x29 TM3 Van der Waals
Stromal cell-derived factor 1 H113 3.29x29 TM3 polar (hydrogen bond)
Stromal cell-derived factor 1 Y116 3.32x32 TM3 Van der Waals
Stromal cell-derived factor 1 Y116 3.32x32 TM3 hydrophobic
Stromal cell-derived factor 1 T117 3.33x33 TM3 Van der Waals
Stromal cell-derived factor 1 L120 3.36x36 TM3 Van der Waals
Stromal cell-derived factor 1 E179 ECL2 Van der Waals
Stromal cell-derived factor 1 D181 ECL2 polar (charge-assisted hydrogen bond)
Stromal cell-derived factor 1 I185 ECL2 Van der Waals
Stromal cell-derived factor 1 D187 45.51x51 ECL2 polar (charge-assisted hydrogen bond)
Stromal cell-derived factor 1 R188 45.52x52 ECL2 polar (charge-assisted hydrogen bond)
Stromal cell-derived factor 1 F189 ECL2 Van der Waals
Stromal cell-derived factor 1 F189 ECL2 aromatic (edge-to-face)
Stromal cell-derived factor 1 Q200 5.39x40 TM5 Van der Waals
Stromal cell-derived factor 1 H203 5.42x43 TM5 Van der Waals
Stromal cell-derived factor 1 Y255 6.51x51 TM6 Van der Waals
Stromal cell-derived factor 1 I259 6.55x55 TM6 hydrophobic
Stromal cell-derived factor 1 L266 6.62x62 TM6 Van der Waals
Stromal cell-derived factor 1 E277 7.28x27 TM7 Van der Waals
Stromal cell-derived factor 1 H281 7.32x31 TM7 Van der Waals
Stromal cell-derived factor 1 E288 7.39x38 TM7 Van der Waals

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Snake plot — Download: PNG | SVG
ICL1 K K L R ICL1ECL1 N W Y F ECL1ICL2 A T N S Q R P R ICL2ECL2 N V S E A D D R Y I C D R F Y P N ECL2ICL3 K G H Q ICL3ECL3 I I K Q ECL3N-term M E G I S I Y T S D N Y T E E M G S G D Y D S M K E P C F N-termC-term S V S R G S S L K I L S K G K R G G H S S V S T E S E S S S F H S S C-term R E E N A N F N K I F L P T I Y S I I F L T G I V G N G L V I L V M G Y Q S M T D K Y R L H L S V A D L L F V I T L P F W A V D A V A G N F L C K A V H V I Y T V N L Y S S V L I L A F I S L D R Y L A I V H K L L A E K V V Y V G V W I P A L L L T I P D F I F A D L W V V V F Q F Q H I M V G L I L P G I V I L S C Y C I I I S K L S H S K R K A L K T T V I L I L A F F A C W L P Y Y I G I S I D S F I L L E G C E F E N T V H K W I S I T E A L A F F H C C L N P I L Y A F L G A K A Q H F K T S A L T
Helix box plot — Download: PNG | SVG G N G V I G T L F I I S Y I T P L F I K 1 L H L S V A D L L F V I T L P F W A V D 2 F A L I L V S S Y L N V T Y I V H V A K 3 E K V V Y V G V W I P A L L L T I P D 4 Y C S L I V I G P L I L G V M I H Q F Q F 5 V I L I L A F F A C W L P Y Y I G I S I 6 I P N L C C H F F A L A E T I S I W K 7

GPCRdb(A)
GPCRdb(A)
CXCR4
TM2
2x60 2.60x60 W94
TM3
3x29 3.29x29 H113
3x32 3.32x32 Y116
3x33 3.33x33 T117
3x36 3.36x36 L120
ECL2
45x51 45.51x51 D187
45x52 45.52x52 R188
TM5
5x40 5.39x40 Q200
5x43 5.42x43 H203
TM6
6x51 6.51x51 Y255
6x55 6.55x55 I259
6x62 6.62x62 L266
TM7
7x27 7.28x27 E277
7x31 7.32x31 H281
7x38 7.39x38 E288